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Very neat, but they're only indexing CRAN and PyPI right now. In my short time doing scientific computing (staff member at a university right now), I've seen a

Very neat, but they're only indexing CRAN and PyPI right now. In my short time doing scientific computing (staff member at a university right now), I've seen a LOT of C and C++, but those don't have canonical package repositories. I think that finding all of those codebases (even if just limited to GitHub) and indexing those would be very interesting and would be necessary to have representation from a few fields.

zbjornson 11y ago
They also seem to be missing Bioconductor, which is where a huge percentage of (maybe even most?) R biology packages are located. Allowing submissions and somehow indexing the relevant repositories in GitHub would be huge.
- jasonpriem 11y ago
  Yep, we chose CRAN for the MVP, since it's the main R package host. But adding other sources is the plan, and Bioconductor is at the top of that list for R.
jasonpriem 11y ago
Yes, agreed...we've had lots of requests to add other languages. And as you say, the growing popularity of GitHub gives us all kinds of cool data even when there's no central package manager for the language. In fact, we're mining imports of every Python and R project on GitHub right now to build out the dependency network beyond the (much much smaller) CRAN and PyPi networks. The idea with Depsy has been to launch quickly with two languages, so people could see what it looks like, then iterate and add more as we get feedback. So we'll count your comment as +1 for C and C++ :)
lutorm 11y ago
I strongly oppose "just limiting to GitHub". If this is to be used as some sort of merit factor, its inclusion can't be contingent on using a particular centralized repo. For a start, there are several such providers. Larger projects might well prefer self-hosting, too.
- dikaiosune 11y ago
  I would oppose it too in the long run, but it would be the easiest low-hanging fruit for getting the ball rolling on including a wider variety of research software, and I was mostly making a suggestion for next steps in developing their (pretty cool) tool. You have to start somewhere, and if you get GitHub working then it would be (hopefully) much easier to then include BitBucket, GitLab, etc. Indexing self-hosted repos would be pretty tricky, I imagine, if only because you'd then need to maintain a list of all of the servers to clone from. Further, there's also the challenge of including software from all of the research groups who don't even appear to use version control, or if they do it's locked away on a private server or service. How does one attribute authorship rights to those people without source history? Anyways, this is a long ramble now, but I'm mostly trying to illustrate that it's difficult to do what Depsy does with software when it's written in languages without a canonical package repository. That doesn't mean they shouldn't try to expand their reach just because "GitHub isn't enough."
  - lutorm 11y ago
    I was kind of figuring that people would register their own software, rather than trying to somehow find them. It doesn't seem much harder accessing different repos on different servers than on just github. You still have to keep an url. Of course, if it's not a public server then you can't do anything, but then again in that case the authors can't really complain they don't get any credit for what they do.

zbjornson 11y ago

They also seem to be missing Bioconductor, which is where a huge percentage of (maybe even most?) R biology packages are located. Allowing submissions and somehow indexing the relevant repositories in GitHub would be huge.

jasonpriem 11y ago
Yep, we chose CRAN for the MVP, since it's the main R package host. But adding other sources is the plan, and Bioconductor is at the top of that list for R.

jasonpriem 11y ago

Yes, agreed...we've had lots of requests to add other languages. And as you say, the growing popularity of GitHub gives us all kinds of cool data even when there's no central package manager for the language. In fact, we're mining imports of every Python and R project on GitHub right now to build out the dependency network beyond the (much much smaller) CRAN and PyPi networks. The idea with Depsy has been to launch quickly with two languages, so people could see what it looks like, then iterate and add more as we get feedback. So we'll count your comment as +1 for C and C++ :)

lutorm 11y ago

I strongly oppose "just limiting to GitHub". If this is to be used as some sort of merit factor, its inclusion can't be contingent on using a particular centralized repo. For a start, there are several such providers. Larger projects might well prefer self-hosting, too.

dikaiosune 11y ago
I would oppose it too in the long run, but it would be the easiest low-hanging fruit for getting the ball rolling on including a wider variety of research software, and I was mostly making a suggestion for next steps in developing their (pretty cool) tool. You have to start somewhere, and if you get GitHub working then it would be (hopefully) much easier to then include BitBucket, GitLab, etc. Indexing self-hosted repos would be pretty tricky, I imagine, if only because you'd then need to maintain a list of all of the servers to clone from. Further, there's also the challenge of including software from all of the research groups who don't even appear to use version control, or if they do it's locked away on a private server or service. How does one attribute authorship rights to those people without source history? Anyways, this is a long ramble now, but I'm mostly trying to illustrate that it's difficult to do what Depsy does with software when it's written in languages without a canonical package repository. That doesn't mean they shouldn't try to expand their reach just because "GitHub isn't enough."
- lutorm 11y ago
  I was kind of figuring that people would register their own software, rather than trying to somehow find them. It doesn't seem much harder accessing different repos on different servers than on just github. You still have to keep an url. Of course, if it's not a public server then you can't do anything, but then again in that case the authors can't really complain they don't get any credit for what they do.